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Pérez-Umphrey AA, Settlecowski AE, Elbers JP, Williams ST, Jonsson CB, Bonisoli-Alquati A, Snider AM, Taylor SS. Genetic variants associated with hantavirus infection in a reservoir host are related to regulation of inflammation and immune surveillance. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 116:105525. [PMID: 37956745 DOI: 10.1016/j.meegid.2023.105525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 10/14/2023] [Accepted: 11/10/2023] [Indexed: 11/15/2023]
Abstract
The immunogenetics of wildlife populations influence the epidemiology and evolutionary dynamic of the host-pathogen system. Profiling immune gene diversity present in wildlife may be especially important for those species that, while not at risk of disease or extinction themselves, are host to diseases that are a threat to humans, other wildlife, or livestock. Hantaviruses (genus: Orthohantavirus) are globally distributed zoonotic RNA viruses with pathogenic strains carried by a diverse group of rodent hosts. The marsh rice rat (Oryzomys palustris) is the reservoir host of Orthohantavirus bayoui, a hantavirus that causes fatal cases of hantavirus cardiopulmonary syndrome in humans. We performed a genome wide association study (GWAS) using the rice rat "immunome" (i.e., all exons related to the immune response) to identify genetic variants associated with infection status in wild-caught rice rats naturally infected with their endemic strain of hantavirus. First, we created an annotated reference genome using 10× Chromium Linked Reads sequencing technology. This reference genome was used to create custom baits which were then used to target enrich prepared rice rat libraries (n = 128) and isolate their immunomes prior to sequencing. Top SNPs in the association test were present in four genes (Socs5, Eprs, Mrc1, and Il1f8) which have not been previously implicated in hantavirus infections. However, these genes correspond with other loci or pathways with established importance in hantavirus susceptibility or infection tolerance in reservoir hosts: the JAK/STAT, MHC, and NFκB. These results serve as informative markers for future exploration and highlight the importance of immune pathways that repeatedly emerge across hantavirus systems. Our work aids in creating cross-species comparisons for better understanding mechanisms of genetic susceptibility and host-pathogen coevolution in hantavirus systems.
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Affiliation(s)
- Anna A Pérez-Umphrey
- School of Renewable Natural Resources, Louisiana State University and AgCenter, 227 RNR Building, Baton Rouge, LA 70803, USA.
| | - Amie E Settlecowski
- School of Renewable Natural Resources, Louisiana State University and AgCenter, 227 RNR Building, Baton Rouge, LA 70803, USA
| | - Jean P Elbers
- School of Renewable Natural Resources, Louisiana State University and AgCenter, 227 RNR Building, Baton Rouge, LA 70803, USA; Institute of Medical Genetics, Center for Pathobiochemistry and Genetics, Medical University of Vienna, Währinger Straße 10, 1090 Vienna, Austria
| | - S Tyler Williams
- School of Renewable Natural Resources, Louisiana State University and AgCenter, 227 RNR Building, Baton Rouge, LA 70803, USA
| | - Colleen B Jonsson
- Department of Microbiology, Immunology and Biochemistry, College of Medicine, University of Tennessee Health Science Center, University of Tennessee, 858 Madison Ave., Memphis, TN 38163, USA
| | - Andrea Bonisoli-Alquati
- School of Renewable Natural Resources, Louisiana State University and AgCenter, 227 RNR Building, Baton Rouge, LA 70803, USA; Department of Biological Sciences, California State Polytechnic University-Pomona, Pomona, CA 91768, USA
| | - Allison M Snider
- School of Renewable Natural Resources, Louisiana State University and AgCenter, 227 RNR Building, Baton Rouge, LA 70803, USA
| | - Sabrina S Taylor
- School of Renewable Natural Resources, Louisiana State University and AgCenter, 227 RNR Building, Baton Rouge, LA 70803, USA
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Mancino M, Lai G, De Grossi F, Cuomo A, Manganaro L, Butta GM, Ferrari I, Vicenzi E, Poli G, Pesce E, Oliveto S, Biffo S, Manfrini N. FAM46C Is an Interferon-Stimulated Gene That Inhibits Lentiviral Particle Production by Modulating Autophagy. Microbiol Spectr 2023; 11:e0521122. [PMID: 37358411 PMCID: PMC10434054 DOI: 10.1128/spectrum.05211-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 06/02/2023] [Indexed: 06/27/2023] Open
Abstract
FAM46C is a multiple myeloma (MM) tumor suppressor whose function is only starting to be elucidated. We recently showed that in MM cells FAM46C triggers apoptosis by inhibiting autophagy and altering intracellular trafficking and protein secretion. To date, both a physiological characterization of FAM46C role and an assessment of FAM46C-induced phenotypes outside of MM are lacking. Preliminary reports suggested an involvement of FAM46C with regulation of viral replication, but this was never confirmed. Here, we show that FAM46C is an interferon-stimulated gene and that the expression of wild-type FAM46C in HEK-293T cells, but not of its most frequently found mutant variants, inhibits the production of both HIV-1-derived and HIV-1 lentiviruses. We demonstrate that this effect does not require transcriptional regulation and does not depend on inhibition of either global or virus-specific translation but rather mostly relies on FAM46C-induced deregulation of autophagy, a pathway that we show to be required for efficient lentiviral particle production. These studies not only provide new insights on the physiological role of the FAM46C protein but also could help in implementing more efficient antiviral strategies on one side and lentiviral particle production approaches on the other. IMPORTANCE FAM46C role has been thoroughly investigated in MM, but studies characterizing its role outside of the tumoral environment are still lacking. Despite the success of antiretroviral therapy in suppressing HIV load to undetectable levels, there is currently no HIV cure, and treatment is lifelong. Indeed, HIV continues to be a major global public health issue. Here, we show that FAM46C expression in HEK-293T cells inhibits the production of both HIV and HIV-derived lentiviruses. We also demonstrate that such inhibitory effect relies, at least in part, on the well-established regulatory role that FAM46C exerts on autophagy. Deciphering the molecular mechanism underlying this regulation will not only facilitate the understanding of FAM46C physiological role but also give new insights on the interplay between HIV and the cellular environment.
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Affiliation(s)
- Marilena Mancino
- INGM, Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, Milan, Italy
| | - Giancarlo Lai
- INGM, Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, Milan, Italy
| | | | - Alessandro Cuomo
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Lara Manganaro
- INGM, Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, Milan, Italy
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Milan, Italy
| | - Giacomo M. Butta
- INGM, Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, Milan, Italy
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Milan, Italy
| | - Ivan Ferrari
- INGM, Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, Milan, Italy
| | - Elisa Vicenzi
- Viral Pathogenesis and Biosafety Unit, San Raffaele Scientific Institute, Milan, Italy
| | - Guido Poli
- Viral Pathogenesis and Biosafety Unit, San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University School of Medicine, Milan, Italy
| | - Elisa Pesce
- INGM, Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, Milan, Italy
| | - Stefania Oliveto
- INGM, Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, Milan, Italy
- Department of Biosciences, University of Milan, Milan, Italy
| | - Stefano Biffo
- INGM, Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, Milan, Italy
- Department of Biosciences, University of Milan, Milan, Italy
| | - Nicola Manfrini
- INGM, Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, Milan, Italy
- Department of Biosciences, University of Milan, Milan, Italy
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Deng J, Xiao W, Wang Z. FAM46C as a Potential Marker for Pan-Cancer Prognosis and Predicting Immunotherapeutic Efficacy. Front Genet 2022; 13:810252. [PMID: 35222533 PMCID: PMC8864238 DOI: 10.3389/fgene.2022.810252] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 01/18/2022] [Indexed: 12/28/2022] Open
Abstract
Background:FAM46C is a common mutated gene in tumours. A comprehensive understanding of the relationship between FAM46C expression and pan-cancer can guide clinical prognosis and broaden the immunotherapeutic targets.Methods: Data from The Cancer Genome Atlas and Genotype-Tissue Expression (GTEx) databases were obtained, and gene expression of different tumour types and stages was analysed. Immunohistochemical analysis was performed to detect differences in the FAM46C protein levels in normal and cancerous tissues. The genetic variation of FAM46C was characterised using cBioPortal. The clinical prognostic value of FAM46C and the impact of FAM46C expression levels on the prognosis of patients with different types of cancer were assessed based on Kaplan–Meier and Cox regression analyses. Gene set enrichment analysis (GSEA) was used to analyse the pathways associated with FAM46C. Correlations between FAM46C expression levels and immune infiltration were assessed using the TIMER2 database and CIBERSORT algorithm, and correlations between FAM46C expression and the ESTIMATE, immune and stromal scores were analysed using the ESTIMATE algorithm. In addition, we also analysed the correlation between FAM46C expression and immune activation, suppression genes and immune chemokines.Results: The expression level of FAM46C was correlated with the prognosis of most tumours, and low expression levels often suggested a poor prognosis. FAM46C was positively correlated with the abundance of CD4+ T cells, CD8+ T cells and plasma B lymphocytes in the tumour microenvironment. FAM46C exhibited a strong correlation with immunomodulatory pathways, immunomodulatory factors and immune markers. In addition, high FAM46C expression correlated with tumour mutational burden in acute myeloid leukaemia and microsatellite instability in endometrial cancer.Conclusion: Our study suggests that FAM46C can be a potential prognostic marker for pan-cancer, is closely associated with immune regulation and may be an immune checkpoint to guide future clinical immunotherapy.
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Affiliation(s)
- Jiehua Deng
- Centre of Imaging Diagnosis, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, China
| | - Wei Xiao
- Department of Clinical Medicine, Medical College of Shihezi University, Shihezi, China
| | - Zheng Wang
- Centre of Imaging Diagnosis, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, China
- *Correspondence: Zheng Wang,
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Bank vole immunoheterogeneity may limit Nephropatia Epidemica emergence in a French non-endemic region. Parasitology 2017; 145:393-407. [PMID: 28931451 DOI: 10.1017/s0031182017001548] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Ecoevolutionary processes affecting hosts, vectors and pathogens are important drivers of zoonotic disease emergence. In this study, we focused on nephropathia epidemica (NE), which is caused by Puumala hantavirus (PUUV) whose natural reservoir is the bank vole, Myodes glareolus. We questioned the possibility of NE emergence in a French region that is considered to be NE-free but that is adjacent to a NE-endemic region. We first confirmed the epidemiology of these two regions and we demonstrated the absence of spatial barriers that could have limited dispersal, and consequently, the spread of PUUV into the NE-free region. We next tested whether regional immunoheterogeneity could impact PUUV chances to circulate and persist in the NE-free region. We showed that bank voles from the NE-free region were sensitive to experimental PUUV infection. We observed high levels of immunoheterogeneity between individuals and also between regions. Antiviral gene expression (Tnf and Mx2) reached higher levels in bank voles from the NE-free region. During experimental infections, anti-PUUV antibody production was higher in bank voles from the NE-endemic region. These results indicated a lower susceptibility to PUUV for bank voles from this NE-free region, which might limit PUUV persistence and therefore, the risk of NE.
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Wan XY, Zhai XF, Jiang YP, Han T, Zhang QY, Xin HL. Antimetastatic effects of norcantharidin on hepatocellular carcinoma cells by up-regulating FAM46C expression. Am J Transl Res 2017; 9:155-166. [PMID: 28123642 PMCID: PMC5250712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 09/12/2016] [Indexed: 06/06/2023]
Abstract
Hepatocellular carcinoma (HCC) is the third leading cause of cancer-related mortality worldwide. Norcantharidin (NCTD), a demethylated analog of cantharidin, possesses antimetastatic effects on HCC cells. The aim of this study was to identify target proteins of NCTD. In this study, we confirmed the antimetastatic effects of NCTD on SMMC-7721 and MHCC-97H cells. Through RNA sequencing, we found a non-canonical poly (A) polymerase, Family-with-sequence-similarity-46C (FAM46C) was up-regulated in response to NCTD exposure. Gene set enrichment analysis on The Cancer Genome Atlas liver HCC (LIHC) dataset revealed that metastasis down pathway was strongly associated with FAM46C expression. Overexpression of FAM46C in HCC cells suppressed cell migration and invasion via suppressing transforming growth factor-β (TGF-β)/Smad signaling and epithelial-mesenchymal transition (EMT) process. Additionally, the antimetastatic effects of NCTD on HCC cells were partially rescued by FAM46C knockdown. Collectively, our results suggested that FAM46C, up-regulated by NCTD treatment, played a critical role in promoting the migration and invasion of HCC cells via TGF-β/Smad signaling. We identified a new therapeutic target of NCTD.
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Affiliation(s)
- Xu-Ying Wan
- The integrated TCM & Western Medicine Department, Eastern Hepatobiliary Surgery Hospital, Second Military Medical UniversityShanghai 200433, P. R. China
| | - Xiao-Feng Zhai
- Department of Traditional Chinese Medicine, Changhai Hospital, Second Military Medical UniversityShanghai 200433, P. R. China
| | - Yi-Ping Jiang
- Department of Pharmacognosy, School of Pharmacy, Second Military Medical UniversityShanghai 200433, P. R. China
| | - Ting Han
- Department of Pharmacognosy, School of Pharmacy, Second Military Medical UniversityShanghai 200433, P. R. China
| | - Qiao-Yan Zhang
- Department of Pharmacognosy, School of Pharmacy, Second Military Medical UniversityShanghai 200433, P. R. China
| | - Hai-Liang Xin
- Department of Pharmacognosy, School of Pharmacy, Second Military Medical UniversityShanghai 200433, P. R. China
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Kuchta K, Muszewska A, Knizewski L, Steczkiewicz K, Wyrwicz LS, Pawlowski K, Rychlewski L, Ginalski K. FAM46 proteins are novel eukaryotic non-canonical poly(A) polymerases. Nucleic Acids Res 2016; 44:3534-48. [PMID: 27060136 PMCID: PMC4857005 DOI: 10.1093/nar/gkw222] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 03/22/2016] [Indexed: 12/22/2022] Open
Abstract
FAM46 proteins, encoded in all known animal genomes, belong to the nucleotidyltransferase (NTase) fold superfamily. All four human FAM46 paralogs (FAM46A, FAM46B, FAM46C, FAM46D) are thought to be involved in several diseases, with FAM46C reported as a causal driver of multiple myeloma; however, their exact functions remain unknown. By using a combination of various bioinformatics analyses (e.g. domain architecture, cellular localization) and exhaustive literature and database searches (e.g. expression profiles, protein interactors), we classified FAM46 proteins as active non-canonical poly(A) polymerases, which modify cytosolic and/or nuclear RNA 3′ ends. These proteins may thus regulate gene expression and probably play a critical role during cell differentiation. A detailed analysis of sequence and structure diversity of known NTases possessing PAP/OAS1 SBD domain, combined with state-of-the-art comparative modelling, allowed us to identify potential active site residues responsible for catalysis and substrate binding. We also explored the role of single point mutations found in human cancers and propose that FAM46 genes may be involved in the development of other major malignancies including lung, colorectal, hepatocellular, head and neck, urothelial, endometrial and renal papillary carcinomas and melanoma. Identification of these novel enzymes taking part in RNA metabolism in eukaryotes may guide their further functional studies.
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Affiliation(s)
- Krzysztof Kuchta
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, Banacha 2C, 02-097 Warsaw, Poland
| | - Anna Muszewska
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Lukasz Knizewski
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland
| | - Kamil Steczkiewicz
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland
| | - Lucjan S Wyrwicz
- Laboratory of Bioinformatics and Biostatistics, M. Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, WK Roentgena 5, 02-781 Warsaw, Poland
| | - Krzysztof Pawlowski
- Department of Experimental Design and Bioinformatics, Warsaw University of Life Sciences, Nowoursynowska 166, 02-787 Warsaw, Poland
| | | | - Krzysztof Ginalski
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland
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